scholarly journals Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 133
Author(s):  
Outi I. Mielonen ◽  
Diogo Pratas ◽  
Klaus Hedman ◽  
Antti Sajantila ◽  
Maria F. Perdomo

Formalin fixation, albeit an outstanding method for morphological and molecular preservation, induces DNA damage and cross-linking, which can hinder nucleic acid screening. This is of particular concern in the detection of low-abundance targets, such as persistent DNA viruses. In the present study, we evaluated the analytical sensitivity of viral detection in lung, liver, and kidney specimens from four deceased individuals. The samples were either frozen or incubated in formalin (±paraffin embedding) for up to 10 days. We tested two DNA extraction protocols for the control of efficient yields and viral detections. We used short-amplicon qPCRs (63–159 nucleotides) to detect 11 DNA viruses, as well as hybridization capture of these plus 27 additional ones, followed by deep sequencing. We observed marginally higher ratios of amplifiable DNA and scantly higher viral genoprevalences in the samples extracted with the FFPE dedicated protocol. Based on the findings in the frozen samples, most viruses were detected regardless of the extended fixation times. False-negative calls, particularly by qPCR, correlated with low levels of viral DNA (<250 copies/million cells) and longer PCR amplicons (>150 base pairs). Our data suggest that low-copy viral DNAs can be satisfactorily investigated from FFPE specimens, and encourages further examination of historical materials.

Molecules ◽  
2020 ◽  
Vol 25 (16) ◽  
pp. 3753 ◽  
Author(s):  
Alexander Basov ◽  
Mikhail Drobotenko ◽  
Alexandr Svidlov ◽  
Eugeny Gerasimenko ◽  
Vadim Malyshko ◽  
...  

In the present study, the effect of 2H/1H isotopic exchange in hydrogen bonds between nitrogenous base pairs on occurrence and open states zones dynamics is investigated. These processes are studied using mathematical modeling, taking into account the number of open states between base pairs. The calculations of the probability of occurrence of open states in different parts of the gene were done depending on the localization of the deuterium atom. The mathematical modeling study demonstrated significant inequality (dependent on single 2H/1H replacement in DNA) among three parts of the gene similar in length of the frequency of occurrence of the open states. In this paper, the new convenient approach of the analysis of the abnormal frequency of open states in different parts of the gene encoding interferon alpha 17 was presented, which took into account both rising and decreasing of them that allowed to make a prediction of the functional instability of the specific DNA regions. One advantage of the new algorithm is diminishing the number of both false positive and false negative results in data filtered by this approach compared to the pure fractile methods, such as deciles or quartiles.


2018 ◽  
Vol 64 (8) ◽  
pp. 1230-1238 ◽  
Author(s):  
Hyunsoo Kim ◽  
Areum Sohn ◽  
Injoon Yeo ◽  
Su Jong Yu ◽  
Jung-Hwan Yoon ◽  
...  

Abstract BACKGROUND Lens culinaris agglutinin-reactive fraction of α-fetoprotein (AFP-L3) is a serum biomarker for hepatocellular carcinoma (HCC). AFP-L3 is typically measured by liquid-phase binding assay (LiBA). However, LiBA does not always reflect AFP-L3 concentrations because of its low analytical sensitivity. Thus, we aimed to develop an analytically sensitive multiple reaction monitoring–mass spectrometry (MRM-MS) assay to quantify AFP-L3 in serum. METHODS The assay entailed the addition of a stable isotope-labeled internal standard protein analog, the enrichment of AFP using a monoclonal antibody, the fractionation of AFP-L3 using L. culinaris agglutinin lectin, deglycosylation, trypsin digestion, online desalting, and MRM-MS analysis. The performance of the MRM-MS assay was compared with that of LiBA in 400 human serum samples (100 chronic hepatitis, 100 liver cirrhosis, and 200 HCC). Integrated multinational guidelines were followed to validate the assay for clinical implementation. RESULTS The lower limit of quantification of the MRM-MS assay (0.051 ng/mL) for AFP-L3 was less than that of LiBA (0.300 ng/mL). Thus, AFP-L3, which was not observed by LiBA in HCC samples (n = 39), was detected by the MRM-MS assay, improving the clinical value of AFP-L3 as a biomarker by switching to a more analytical sensitive platform. The method was validated, meeting all the criteria in integrated multinational guidelines. CONCLUSIONS Because of the lower incidence of false-negative findings, the MRM-MS assay is more suitable than LiBA for early detection of HCC.


Author(s):  
Sanjeev Kumar ◽  
Jagan Mohanarao Gali ◽  
T.K. Dutta ◽  
P. Roychoudhury ◽  
P.K. Subudhi

Background: Diarroeagenic Escherichia coli (DEC) including enteropathogenic E. coli (EPEC) and enterohaemorrhagic E. coli (EHEC) is associated with acute diarrhoea in children and young animals. The virulence is associated with attaching and effacing lesions encoded by eaeA gene is considered as marker for EPEC and EHEC. Laboratory diagnosis of such infections is carried out by traditional bacteriological techniques and by conventional PCR assays. Those techniques often provide false negative result and at the same time are costly as well as difficult to perform in the field level. The loop-mediated isothermal amplification (LAMP) is a new generation DNA amplification assay is developed for detection of eaeA gene in E. coli isolated from diarrhoeic piglets.Methods: Samples were collected from diarrhoeic piglets for isolation and identification of E. coli. eaeA gene was detected by conventional PCR using specific primers in all the isolates. LAMP assay was standardized for detection of eaeA gene. Analytical sensitivity of LAMP was evaluated using 10 fold serially diluted E. coli genomic DNA. The specificity of the LAMP assay was determined by evaluating the cross reactivity with 19 other enteric and non-enteric bacterial species. Standardized LAMP was applied for detection of eaeA gene in the field isolates.Result: A total of 37 (24.67%) isolates were recorded as positive for eaeA gene by conventional PCR, while 49 (32.67%) isolates were recorded as positive for eaeA gene by LAMP assay. The LAMP assay was 10 times more sensitive than conventional PCR. LAMP assay was found to be more sensitive, specific, cost effective, user friendly and reliable technique over conventional PCR, which can be applied for screening of the clinical isolates for confirmation of EPEC and/or EHEC.


2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Yoonjung Kim ◽  
Mi-Soon Han ◽  
Juwon Kim ◽  
Aerin Kwon ◽  
Kyung-A Lee

A total of 84 nasopharyngeal swab specimens were collected from 84 patients. Viral nucleic acid was extracted by three automated extraction systems: QIAcube (Qiagen, Germany), EZ1 Advanced XL (Qiagen), and MICROLAB Nimbus IVD (Hamilton, USA). Fourteen RNA viruses and two DNA viruses were detected using the Anyplex II RV16 Detection kit (Seegene, Republic of Korea). The EZ1 Advanced XL system demonstrated the best analytical sensitivity for all the three viral strains. The nucleic acids extracted by EZ1 Advanced XL showed higher positive rates for virus detection than the others. Meanwhile, the MICROLAB Nimbus IVD system was comprised of fully automated steps from nucleic extraction to PCR setup function that could reduce human errors. For the nucleic acids recovered from nasopharyngeal swab specimens, the QIAcube system showed the fewest false negative results and the best concordance rate, and it may be more suitable for detecting various viruses including RNA and DNA virus strains. Each system showed different sensitivity and specificity for detection of certain viral pathogens and demonstrated different characteristics such as turnaround time and sample capacity. Therefore, these factors should be considered when new nucleic acid extraction systems are introduced to the laboratory.


2021 ◽  
Vol 83 (3) ◽  
pp. 66-71
Author(s):  
А.Y. Horlov ◽  
◽  
V.H. Serdiuk ◽  
О.K. Kiselova ◽  
A.O. Shevchuk ◽  
...  

A novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease (COVID)-19, that emerged as a major pandemic. SARS-CoV-2 was identified as a betacoronavirus. Nucleocapsid protein (NP) is evolutionary high protein homologies and solid structure protein for SARS-CoV-2 detection as opposed to other proteins, that aren`t reliable as a single viral antigen during diagnostics methods. The viral RNA can be detected from nasal and pharyngeal swabs and bronchoalveolar lavage samples by PCR assay. However, the wrong collection of samples can lead to false-negative diagnosis and have dangerous consequences at this stage of pandemic. One of efficient and accurate methodological approaches for the screening of pathogens are serological assays. Aim. Evaluation and comparison of the sensitivity of invented DIA®-SARS-CoV-2-Ag-R enzyme-linked immunosorbent assay (ELISA)-based test system and commercial rapid tests, which detect the viral antigen of SARS-CoV-2. Methods. We carried out a comparison of DIA®-SARS-CoV-2-Ag-R and existed commercial test systems, which are used to detect the antigen of SARS-CoV-2 virus. Rapid tests are intended for nasopharyngeal swabs, but we proposed a protein of our own manufacture – recombinant NP as a calibrator. The detection limit was calibrated by standard CFAR #100982 NIBSC, UK. We had determined levels of NP (1400, 900, 750, 640 and 280 pg/mL) that we used as a sample for the rapid tests. The COVID-19 Ag Rapid Tests were performed according to the manufactures instructions at room temperature. Results. DIA®-SARS-CoV-2-Ag-R detected 10 pg/mL of in-house standard of recombinant SARS-CoV-2 NP. The positive results were observed using 1400, 900, 750 pg/mL, while 640 and 280 pg/mL samples were performed as negative in ABBOTT-PanBio test. The rapid tests manufactured by МBU, BIOTIME, Core Technology, SD BIOSENSOR and Turklab showed positive results only in 1400 pg/mL concentration. NP of lower levels was detected as a negative sample. The LEPU MEDICAL test was evaluated as positive sample using 900 pg/mL. The rapid test manufactured by Green Cross Medical Science Corp. showed negative results for all levels of NP. It can mean that the sensitivity of test is lower and demands higher level of antigen to detect the presence of SARS-CoV-2. Conclusions. The study presented an excellent analytical sensitivity of DIA®-SARS-CoV-2-Ag-R against commercial Antigen rapid tests. Thus, invented ELISA test system can be recommended for widespread usage for detection and confirmation of acute stage of SARS-CoV-2 infection.


Author(s):  
Niccolò Alfano ◽  
Anisha Dayaram ◽  
Jan Axtner ◽  
Kyriakos Tsangaras ◽  
Marie-Louise Kampmann ◽  
...  

ABSTRACTEnvironmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively to mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA have been applied to monitor known wildlife pathogens, however, most wildlife pathogens are unknown and often evolutionarily divergent.To detect and identify known and novel mammalian viruses from eDNA/iDNA sources, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high throughput sequencing.We detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes.Our results demonstrate that eDNA/iDNA samples represent an effective non-invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kesheng Li ◽  
Chongxiang Tong ◽  
Xiaoqin Ha ◽  
Chaoning Zeng ◽  
Xia Chen ◽  
...  

Abstract Background The novel coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has quickly spread worldwide since its outbreak in December 2019. One of the primary measures for controlling the spread of SARS-CoV-2 infection is an accurate assay for its diagnosis. SARS-CoV-2 real-time PCR kits suffer from some limitations, including false-negative results in the clinic. Therefore, there is an urgent need for the development of a rapid antibody test kit for COVID-19 diagnosis. Methods The nuclear capsid protein (N) and spike protein 1 (S1) fragments of SARS-CoV-2 were expressed in Escherichia coli, and rapid antibody-based tests for the diagnosis of SARS-CoV-2 infection were developed. To evaluate their clinical applications, the serum from COVID-19 patients, suspected COVID-19 patients, recovering COVID-19 patients, patients with general fever or pulmonary infection, doctors and nurses who worked at the fever clinic, and health professionals was analyzed by the rapid antibody test kits. The serum from patients infected with Mycoplasma pneumoniae and patients with respiratory tract infection was further analyzed to test its cross-reactivity with other respiratory pathogens. Results A 47 kDa N protein and 67 kDa S1 fragment of SARS-CoV-2 were successfully expressed, purified, and renatured. The rapid antibody test with recombinant N protein showed higher positive rate than the rapid IgM antibody test with recombinant S1 protein. Clinical evaluation showed that the rapid antibody test kit with recombinant N protein had 88.56 % analytical sensitivity and 97.42 % specificity for COVID-19 patients, 53.48 % positive rate for suspected COVID-19 patients, 57.14 % positive rate for recovering COVID-19 patients, and 0.5−0.8 % cross-reactivity with other respiratory pathogens. The analytical sensitivity of the kit did not significantly differ in COVID-19 patients with different disease courses (p < 0.01). Conclusions The rapid antibody test kit with recombinant N protein has high specificity and analytical sensitivity, and can be used for the diagnosis of SARS-CoV-2 infection combined with RT-PCR.


2021 ◽  
Author(s):  
Verena Haage ◽  
Edmilson Ferreira de Oliveira-Filho ◽  
Andres Moreira-Soto ◽  
Arne Kühne ◽  
Carlo Fischer ◽  
...  

AbstractRapid antigen-detecting tests (Ag-RDTs) can complement molecular diagnostics for COVID-19. The recommended temperature for storage of SARS-CoV-2 Ag-RDTs ranges between 5-30°C. In many countries that would benefit from SARS-CoV-2 Ag-RDTs, mean temperatures exceed 30°C. We assessed analytical sensitivity and specificity of eleven commercially available SARS-CoV-2 Ag-RDTs using different storage and operational temperatures, including (i) long-term storage and testing at recommended conditions, (ii) recommended storage conditions followed by 10 minutes exposure to 37°C and testing at 37°C and (iii) 3 weeks storage followed by testing at 37°C. The limits of detection of SARS-CoV-2 Ag-RDTs under recommended conditions ranged from 8.2×105-7.9×107 genome copies/ml of infectious SARS-CoV-2 cell culture supernatant. Despite long-term storage at recommended conditions, 10 minutes pre-incubation of Ag-RDTs and testing at 37°C resulted in about ten-fold reduced sensitivity for 46% of SARS-CoV-2 Ag-RDTs, including both Ag-RDTs currently listed for emergency use by the World Health Organization. After 3 weeks of storage at 37°C, 73% of SARS-CoV-2 Ag-RDTs exhibited about ten-fold reduced sensitivity. Specificity of SARS-CoV-2 Ag-RDTs using cell culture-derived human coronaviruses HCoV-229E and HCoV-OC43 was not affected by storage and testing at 37°C. In summary, short- and long-term exposure to elevated temperatures likely impairs sensitivity of several SARS-CoV-2 Ag-RDTs that may translate to false-negative test results at clinically relevant virus concentrations compatible with inter-individual transmission. Ensuring appropriate transport and storage conditions, and development of tests that are more robust across temperature fluctuations will be important for accurate use of SARS-CoV-2 Ag-RDTs in tropical settings.


Author(s):  
Stephen Tahan ◽  
Bijal A. Parikh ◽  
Lindsay Droit ◽  
Meghan A. Wallace ◽  
Carey-Ann D. Burnham ◽  
...  

Diagnostic assays for detecting SARS-CoV-2 are essential for patient management, infection prevention, and the public health response for COVID-19. The efficacy and reliability of these assays are of paramount importance in both tracking and controlling spread of the virus. Real-time RT-PCR assays rely on a fixed genetic sequence for primers and probe binding. Mutations can potentially alter the accuracy of these assays and lead to unpredictable analytical performance characteristics and false-negative results. Herein, we identify a G-to-U transversion (nucleotide 26372) in the SARS-CoV-2 E gene in three specimens with reduced viral detection efficiency using a widely available commercial assay. Further analysis of the public GISAID repository led to the identification of 18 additional genomes with this mutation, which reflect five independent mutational events. This work supports the use of dual-target assays to reduce the number of false-negative PCR results.


2003 ◽  
Vol 15 (3) ◽  
pp. 281-285 ◽  
Author(s):  
Michel Pépin ◽  
Philippe Dufour ◽  
Maurice Lambert ◽  
Michel Aubert ◽  
Aurèle Valognes ◽  
...  

Serologic diagnosis of ovine contagious agalactia ( Mycoplasma agalactiae) with the enzyme-linked immunosorbent assay (ELISA) developed by Agence Française de Séceurité Sanitaire des Aliments (AFS-SA) may produce a few false-positive (FP) and false-negative (FN) results. When the prevalence of disease is low, these erroneous results may generate problems for eradication schemes. To prevent this, 2 commercial ELISAs were compared with the AFSSA ELISA. Flocks of known status were selected and classified into 4 categories: true positive (TP), FP, true negative (TN), and FN; 20 sheep per flock were submitted for blood sampling. A flock was considered positive when at least 1 out of 20 sera was positive or 2 sera were doubtful. In the flock, the diagnostic sensitivity of the 3 kits was very good (100%), and the diagnostic specificity showed an improvement from 46% (AFSSA test) to 88% and 92% (commercial tests). Considering individual animals, very few positive ewes were detected within TN or FP flocks; the proportion of positive ewes varied greatly from one kit to another (48% to 82%) within TP flocks. The kinetics of antibody response in sheep experimentally infected with various field strains of M. agalactiae were quite similar with all 3 ELISAs. The agreement between the 3 tests, assessed using the kappa value, varied from moderate to good (respective values of 0.56, 0.61, and 0.86). The 2 commercial ELISAs showed better performances, probably because of a superior analytical sensitivity, and are a good alternative for the serodiagnosis of contagious agalactia in sheep.


Sign in / Sign up

Export Citation Format

Share Document